Hi @jorge_garcia and thank you for responding. I do always appreciate your input even I get grumpy from time to time.
Yes, I always open and close from the master document, and I leave all files open throughout. I don't normally even bother with the synchronizer because it hasn't been necessary. The only reason I ran it this time was because Fusion broke my design and severed the connection between Schematic and Layout.
In more detail - I can find the original breakage from the history if necessary so you can look for yourself (as a private share):
I had just finished routing some high frequency traces in Layout. I then went back to schematic to rework one of the sheets that had yet to be laid out (components were outside the board perimeter). This rework involved removing most of the existing components on the sheet - Almost complete redesign. Having finished deleting old and adding the new components/wiring I then noticed that the files had gone out of sync. This was where it all started falling apart badly.
Fusion complained that several nets in the Layout were Unknown. I used the Inspector to remove them. This uncovered more unknowns which I progressively removed from the Layout. Eventually it went back to reporting the first net again, although which was already removed. Selecting that net name in the Inspector showed that there were no connections and there was nothing to delete. Yet the issue persisted and the signal continued to be listed in Inspector despite not actually being there in the Layout.
Eventually I tried to remove the entire problem block (the problem area was an instantiated module), by deleting the instance from the schematic. This removed the components from the layout but immediately reinstated them all again outside the board perimeter, but without the module prefix. The components did not even exist in the schematic any longer because there were no instances of the module. And yet even if I deleted them manually from the layout they just got reinserted at the next sync.
I was left with no option but to rewind the design. Because of the prior issues I felt it was sensible to run synchronize just to be sure everything was ok. Which brought me to the new issue where Synchronize just reported an error. So, not in fact ok.